Man pages for Aufiero/circRNAprofiler
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
| ahChainFiles | ahChainFile |
| ahRepeatMasker | ahRepeatMasker |
| annotateBSJs | Annotate circRNA features. |
| annotateRepeats | Annotate repetitive elements |
| annotateSNPsGWAS | Annotate GWAS SNPs |
| attractSpecies | attractSpecies |
| backSplicedJunctions | backSplicedJunctions |
| checkProjectFolder | Check project folder |
| filterCirc | Filter circRNAs |
| formatGTF | Format annotation file |
| getBackSplicedJunctions | Import detected circRNAs |
| getCircSeqs | Retrieve circRNA sequences |
| getDeseqRes | Differential circRNA expression analysis adapted from DESeq2 |
| getDetectionTools | Create data frame with circRNA detection codes |
| getEdgerRes | Differential circRNA expression analysis adapted from EdgeR |
| getMiRsites | Screen target sequences for miR binding sites |
| getMotifs | Screen target sequences for recurrent motifs |
| getRandomBSJunctions | Retrieve random back-spliced junctions |
| getRegexPattern | Convert IUPAC sequence to an regular expression |
| getSeqsAcrossBSJs | Retrieve back-spliced junction sequences |
| getSeqsFromGRs | Retrieve sequences flanking back-spliced junctions |
| gtf | gtf |
| gwasTraits | gwasTraits |
| importCircExplorer2 | Import circRNAs detected by CircExplorer2 |
| importCircMarker | Import circRNAs detected by CircMarker |
| importKnife | Import circRNAs detected by KINFE |
| importMapSplice | Import circRNAs detected by MapSplice2 |
| importNCLscan | Import circRNAs detected by NCLscan |
| importOther | Import circRNAs detected by an annotation-based circRNA... |
| importUroborus | Import circRNAs detected by UROBORUS |
| initCircRNAprofiler | Initialize the project folder |
| iupac | iupac |
| liftBSJcoords | LiftOver back-spliced junction coordinates |
| memeDB | memeDB |
| mergeBSJunctions | Group circRNAs identified by multiple prediction tools |
| mergedBSJunctions | mergedBSJunctions |
| mergeMotifs | Group motifs shared by multiple RBPs |
| miRspeciesCodes | miRspeciesCodes |
| plotExBetweenBSEs | Plot exons between back-spliced junctions |
| plotExPosition | Plot back-spliced exon positions |
| plotHostGenes | Plot circRNA host genes |
| plotLenBSEs | Plot length back-spliced exons |
| plotLenIntrons | Plot length introns flanking back-spliced junctions |
| plotMiR | Plot miRNA analysis results |
| plotMotifs | Plot motifs analysis results |
| plotTotExons | Plot exons in the circRNA host transcript |
| rearrangeMiRres | Rearrange miR results |
| volcanoPlot | Plot differential circRNA expression results |
